Single-Molecule Approaches to Study DNA Condensation

Research output: Contribution to book/conference proceedings/anthology/reportChapter in book/anthology/reportContributedpeer-review



Proteins drive genome compartmentalization across different length scales. While the identities of these proteins have been well-studied, the physical mechanisms that drive genome organization have remained largely elusive. Studying these mechanisms is challenging owing to a lack of methodologies to parametrize physical models in cellular contexts. Furthermore, because of the complex, entangled, and dense nature of chromatin, conventional live imaging approaches often lack the spatial resolution to dissect these principles. In this chapter, we will describe how to image the interactions of λ-DNA with proteins under purified and cytoplasmic conditions. First, we will outline how to prepare biotinylated DNA, functionalize coverslips with biotin-conjugated poly-ethylene glycol (PEG), and assemble DNA microchannels compatible for the imaging of protein-DNA interactions using total internal fluorescence microscopy. Then we will describe experimental methods to image protein-DNA interactions in vitro and DNA loop extrusion using Xenopus laevis egg extracts.


Original languageEnglish
Title of host publicationCell Cycle Control
EditorsAnna Castro, Benjamin Lacroix
PublisherHumana Press
Number of pages19
ISBN (electronic)978-1-0716-3557-5
ISBN (print)978-1-0716-3559-9, 978-1-0716-3556-8
Publication statusPublished - 24 Feb 2024

Publication series

SeriesMethods in Molecular Biology (MIMB; Vol. 2740)

External IDs

PubMed 38393466


ASJC Scopus subject areas


  • Genome organization, In vitro biochemistry, Loop extrusion, Lysate-based approaches, Quantitative imaging, Single-molecule biophysics, TIRF microscopy, Xenopus laevis, Animals, DNA Packaging, Chromatin/genetics, DNA, Chromosomes

Library keywords